Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 141

10 diseases · 23 shared-gene connections
10 Diseases
27 Unique genes
0.242 Avg. similarity score
Deafness enamel hypoplasia nail defects Most-connected disease (7 links)
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Disease Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Deafness enamel hypoplasia nail defects 7 7 2
Deafness-enamel hypoplasia-nail defects syndrome 7 7 2
Heimler syndrome 7 7 4
Peroxisome biogenesis disorder 5 5 24
Spinocerebellar ataxia blindness deafness syndrome 5 5 1
Zellweger spectrum disorder 5 5 13
Central nervous system demyelinating disease 4 4 4
peroxisome biogenesis disorder due to PEX1 defect 3 3 1
dilated cardiomyopathy 2B 2 2 1
megalencephalic leukoencephalopathy with subcortical cysts 1 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
PEX6 7 / 10 Central nervous system demyelinating disease, Deafness enamel hypoplasia nail defects, Deafness-enamel hypoplasia-nail defects syndrome, Heimler syndrome and 3 more
PEX1 6 / 10 Deafness enamel hypoplasia nail defects, Deafness-enamel hypoplasia-nail defects syndrome, Heimler syndrome, Peroxisome biogenesis disorder and 2 more
GATAD1 3 / 10 dilated cardiomyopathy 2B, Heimler syndrome, Peroxisome biogenesis disorder
PEX26 3 / 10 Heimler syndrome, Peroxisome biogenesis disorder, Zellweger spectrum disorder
MLC1 2 / 10 Central nervous system demyelinating disease, megalencephalic leukoencephalopathy with subcortical cysts 1
PEX10 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX11B 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX12 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX13 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX14 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX16 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX19 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX2 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX3 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
PEX5 2 / 10 Peroxisome biogenesis disorder, Zellweger spectrum disorder
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Peroxisome
PEX6, PEX1, PEX26, PEX10, PEX11B, PEX12, PEX13, PEX14, PEX16, PEX19, PEX2, PEX3
 KEGG 17 / 83 91.1× 2.61e-31 8.23e-28 ✓ sig.
Class I peroxisomal membrane protein import
PEX26, PEX11B, PEX12, PEX13, PEX14, PEX16, PEX19, PEX2, PEX3, ABCD1
 Reactome 10 / 20 222× 8.98e-23 1.18e-19 ✓ sig.
Peroxisomal protein import
PEX6, PEX1, PEX26, PEX10, PEX12, PEX13, PEX14, PEX2, PEX5, PEX7
 Reactome 10 / 63 70.6× 5.87e-17 2.77e-14 ✓ sig.
E3 ubiquitin ligases ubiquitinate target proteins
PEX10, PEX12, PEX13, PEX14, PEX2, PEX5, PAF1
 Reactome 7 / 59 52.8× 3.93e-11 6.21e-9 ✓ sig.
ABC transporters in lipid homeostasis
PEX19, PEX3, ABCD1
 Reactome 3 / 18 74.1× 8.08e-6 2.81e-4 ✓ sig.
Defective ABCD1 causes adrenoleukodystrophy (ALD)
ABCD1
 Reactome 1 / 1 445× 2.25e-3 2.48e-2 ✓ sig.
Defective MMAA causes methylmalonic aciduria type cblA
MMUT
 Reactome 1 / 2 222× 4.49e-3 4.08e-2 ✓ sig.
Defective MUT causes methylmalonic aciduria mut type
MMUT
 Reactome 1 / 2 222× 4.49e-3 4.08e-2 ✓ sig.
Propionyl-CoA catabolism
MMUT
 Reactome 1 / 5 89.0× 1.12e-2 7.34e-2
Linoleic acid (LA) metabolism
ABCD1
 Reactome 1 / 8 55.6× 1.78e-2 9.67e-2
Pexophagy
PEX5
 Reactome 1 / 10 44.5× 2.23e-2 1.09e-1
Beta-oxidation of very long chain fatty acids
ABCD1
 Reactome 1 / 11 40.4× 2.45e-2 1.15e-1
alpha-linolenic acid (ALA) metabolism
ABCD1
 Reactome 1 / 13 34.2× 2.88e-2 1.26e-1
Mitochondrial tRNA aminoacylation
DARS2
 Reactome 1 / 14 31.8× 3.10e-2 1.31e-1
Cobalamin transport and metabolism
MMUT
 KEGG 1 / 18 24.7× 3.97e-2 1.51e-1

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
peroxisome organization
PEX6, PEX1, PEX10, PEX11B, PEX12, PEX14, PEX16, PEX19, PEX2, PEX3, PEX5, PEX7
 GO:0007031 14 / 23 421× 2.25e-36 1.83e-32 ✓ sig.
protein import into peroxisome matrix
PEX6, PEX1, PEX26, PEX10, PEX12, PEX13, PEX14, PEX16, PEX2, PEX5, PEX7
 GO:0016558 11 / 14 544× 1.95e-30 1.07e-26 ✓ sig.
protein import into peroxisome matrix, receptor recycling
PEX6, PEX1, PEX26, PEX10, PEX12, PEX13, PEX14, PEX2, PEX5
 GO:0016562 9 / 10 623× 6.13e-26 2.12e-22 ✓ sig.
protein unfolding
PEX6, PEX1, PEX26, PEX10, PEX12, PEX13, PEX14, PEX2, PEX5
 GO:0043335 9 / 12 519× 1.35e-24 4.02e-21 ✓ sig.
protein targeting to peroxisome
PEX6, PEX1, PEX12, PEX16, PEX19, PEX5, PEX7
 GO:0006625 7 / 10 484× 6.74e-19 9.10e-16 ✓ sig.
protein import into peroxisome matrix, substrate release
PEX10, PEX12, PEX13, PEX14, PEX2, PEX5
 GO:0044721 6 / 6 692× 5.01e-18 6.04e-15 ✓ sig.
protein import into peroxisome membrane
PEX26, PEX16, PEX19, PEX3, PEX5
 GO:0045046 5 / 6 577× 2.55e-14 1.54e-11 ✓ sig.
protein import into peroxisome matrix, translocation
PEX6, PEX13, PEX14, PEX5
 GO:0016561 4 / 4 692× 3.46e-12 1.40e-9 ✓ sig.
cellular response to reactive oxygen species
PEX10, PEX12, PEX13, PEX14, PEX2, PEX5
 GO:0034614 6 / 45 92.3× 3.93e-11 1.24e-8 ✓ sig.
protein monoubiquitination
PEX10, PEX12, PEX13, PEX14, PEX2, PEX5
 GO:0006513 6 / 55 75.5× 1.39e-10 3.86e-8 ✓ sig.
peroxisome fission
PEX11B, PEX19, PEX11A, PEX11G
 GO:0016559 4 / 12 231× 1.70e-9 3.59e-7 ✓ sig.
peroxisome membrane biogenesis
PEX16, PEX19, PEX11A
 GO:0016557 3 / 3 692× 2.69e-9 5.36e-7 ✓ sig.
regulation of peroxisome size
PEX11B, PEX11A, PEX11G
 GO:0044375 3 / 3 692× 2.69e-9 5.36e-7 ✓ sig.
pexophagy
PEX10, PEX12, PEX2, PEX5
 GO:0000425 4 / 18 154× 1.04e-8 1.78e-6 ✓ sig.
protein import into peroxisome matrix, docking
PEX13, PEX14, PEX5
 GO:0016560 3 / 4 519× 1.07e-8 1.82e-6 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Peroxisome biogenesis disorder Zellweger spectrum disorder 0.520 13 5.71e-39 2.45e-37 ✓ sig.
Heimler syndrome Peroxisome biogenesis disorder 0.160 4 4.54e-12 5.43e-11 ✓ sig.
Heimler syndrome Zellweger spectrum disorder 0.200 3 1.88e-9 1.75e-8 ✓ sig.
Deafness enamel hypoplasia nail defects Deafness-enamel hypoplasia-nail defects syndrome 0.667 2 8.44e-9 7.20e-8 ✓ sig.
Deafness enamel hypoplasia nail defects Heimler syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Heimler syndrome 0.400 2 5.06e-8 3.92e-7 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Zellweger spectrum disorder 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Deafness enamel hypoplasia nail defects Zellweger spectrum disorder 0.143 2 6.58e-7 4.21e-6 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Peroxisome biogenesis disorder 0.080 2 2.33e-6 1.35e-5 ✓ sig.
Deafness enamel hypoplasia nail defects Peroxisome biogenesis disorder 0.080 2 2.33e-6 1.35e-5 ✓ sig.
Deafness enamel hypoplasia nail defects Spinocerebellar ataxia blindness deafness syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness enamel hypoplasia nail defects peroxisome biogenesis disorder due to PEX1 defect 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome Spinocerebellar ataxia blindness deafness syndrome 0.333 1 1.30e-4 3.90e-4 ✓ sig.
Deafness-enamel hypoplasia-nail defects syndrome peroxisome biogenesis disorder due to PEX1 defect 0.333 1 1.30e-4 3.90e-4 ✓ sig.
dilated cardiomyopathy 2B Heimler syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Heimler syndrome peroxisome biogenesis disorder due to PEX1 defect 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Heimler syndrome Spinocerebellar ataxia blindness deafness syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Central nervous system demyelinating disease Spinocerebellar ataxia blindness deafness syndrome 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Central nervous system demyelinating disease megalencephalic leukoencephalopathy with subcortical cysts 1 0.200 1 2.60e-4 6.40e-4 ✓ sig.
Central nervous system demyelinating disease Deafness-enamel hypoplasia-nail defects syndrome 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Central nervous system demyelinating disease Deafness enamel hypoplasia nail defects 0.167 1 5.19e-4 1.04e-3 ✓ sig.
Spinocerebellar ataxia blindness deafness syndrome Zellweger spectrum disorder 0.071 1 8.44e-4 1.48e-3 ✓ sig.
dilated cardiomyopathy 2B Peroxisome biogenesis disorder 0.040 1 1.56e-3 2.36e-3 ✓ sig.